Dear experts,

In the recommended reconstructions ( http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) it is stated that one should do CPs first and than do skullstripping. Why is that?

However the recon-all after CPs (recon-all -autorecon2-cp -autorecon3 -subjid) includes less (or later) stages from the autorecon process (only stages 12-31) than the recon-all after skullstripping (recon-all -autorecon2 -autorecon3 -subjid) (stages 6-31) does. Wouldn't this indicate that skullstripping should be done before applying CPs?

Best regards Thomas